Deformation: Biomechanics

What is and how would you break apart a primary protein structure

Sequence of amino acids: Chemical attack to break apart bonds

What is and how would you break apart a secondary protein structure

Non-chemical bonds between backbone elements: vulnerable to denaturation

What is and how would you break apart a tertiary protein structure

Disulphide bridges & non-chemical bonds between R-groups: vulnerable to denaturation

What is and how would you break apart a quaternary protein structure

Protein aggregation: vulnerable to denaturation and separation

Describe hydrolysis

Nucleophilic attack. Reaction begins with oxygen of water targeting the partially positive amide carbon

Describe the likelihood of a hydrolysis reaction happening

Thermodynamically favourable (releases energy), but has a relatively large barrier. So natural decay process is slow, but lots of things can accelerate or decelerate this.

How vulnerable are sugars to hydrolysis

Not as vulnerable, generally need acidic/basic conditions to drive process. Eg stomach acid for digestion

How vulnerable is DNA to hydrolysis

Phosphate linker very vulnerable to hydrolysis, far larger local charge and polarity, need to avoid heat and pH changes to keep stable, DNA protected by supercoiling

What is deamidation

Change of chemical structure, the conversion of amino acid R-chain amide groups. Decay process could involve loss of function through changes in functional groups eg. deamidation rather than direct bond breaking of chain or structure loss

What is denaturisation

Unfolding protein process exposes hydrophobic parts of molecule to water. Leads to protein chain aggregation to avoid hydrophobic energetic penalties, coagulation process

What 5 processes can cause denaturation

pH changes, temperature, stresses, additives (molecules + ions), solvent

How does a change in pH cause denaturation

Presence of H+ and OH- will interact with functional groups/polar groups disrupting H-bond network and potentially some dipole interactions

How does a change in temperature cause denaturation

More heat into the system will overcome enthalpy associated with inter/intra molecular interactions (eg H bonds) causing general structural loss

How does a change in solvent cause denaturation

Water molecules are often key components of a protein structure, structured water, making specific H bonds between regions with long lifetimes. Changing the solvent will alter the potential to form these interactions

How does a change in stress cause denaturation

Mechanical force to the solution and specifically the molecule will pull the structure apart

Causes of denaturation

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Define a free radical

Atom with an unpaired electron, can form in many species which are under bonded

Why are free radicals very reactive

E- in unpaired orbital very active causes then to attack generally stable bonded as not energy driven process

When are free radicals produced?

When bonds are split homiletically (even distribution of e-). Enough energy must be injected into a bond to promote e- into anti-bonding orbitals causing bond to break. Need high energy - UV or heat

What breakdown of molecular systems is associated with food decay?

Free radicals

How can be free radicals be controlled/stabilised?

Inhibiting free radicals by generating dislocation across a molecule eg. resonance structures generated by benzyl ring

Explain how vitamin E affects free radicals

Presence of phenol group to adsorb (mop up) free radical. Acts as a natural preservative since absorbs the free radicals preventing their decay process from occurring

Explain the J-shaped curve

Initially very easy to deform (malleable), then becomes very stiff and large energy needed to take material to failure point

Explain the structure of collagen

Molecular triple helix - 3 collagen chains entwinned

Explain the 'toe region' of a collagen stress strain graph

Fibres can easily stretch out and lose crimping as we apply stress - does not break bonds or damages structure

Explain the plastic region of a collagen stress strain graph

Stiff region - fibres/fibrils slide past each other breaking intermolecular interactions so more force/energy required. Irreversible extension occurs.

Explain the linear region of a collagen stress stain graph

Linear reversible behaviour up to the yield point as the collagen molecules are stretched

Explain the failure of collagen on a stress strain graph

The fibres themselves fail, either together or one after another showing progressive tearing

What is the effect of water on collagen.

Water can act as lubricant between chains by mediating the interactions between chains it is then more labile and able to shift in position. So changes to environment eg. humidity can change properties

What is and are the effects of pre-stressing in collagen

Pre stressing is to begin via a tension/compression of the collagen to move it to a stiffer region. Used in eg arteries since needs to be stiffer

What is viscoelastic behaviour?

After deformation removal material returns to shape over a period of time. Dynamic process

Why has alpha helix got viscoelastic properties compared to beta sheet

Alpha helix can be stretched, squashed, bent to new conformation but will gradually return due to give in structure compared to beta sheet. Beta sheets habe lots of regular H bonds which create semi crystalline system

For viscoelastic properties does system need to be disordered

No, need system with preferred conformation not naturally disordered

What does a viscoelastic materials stress strain curve look like

Hysteresis loop because materials absorb energy as molecules reorganise and move

Explain the large energy loss in a viscoelastic hysteresis loop and why its beneficial

Energy dissipated is good as it operates in a cushioning way and avoids energy going into eg crack propagation making the material tougher as it can absorb impacts and deformations

Give two examples of materials in the body which utilise the energy loss in viscoelastic hysteresis

Cartilage around joints. This can absorb the energy associated with impact as limbs move. Ground substance found to cushion around organs

What is tan theta

The related loss due to the time delay in the materials responding to stress

Give some examples where keratin is the key mechanical protein

Hair, hooves, feathers, reptile skin, claws

How do the α-helix and β-sheet operate in keratin

α-helix operates as the viscous region. It can stretch, twist, and bend. β-sheet is more elastic operates more like a solid phase

What happens if you increase the α-helix content in keratin

Will generate a larger viscous behaviour. Keratin becomes more stretchy, better able to absorb impacts eg hair, horns

What happens if you increase the β-sheet content in keratin

Generate more rigid standard elastic response. Better for a harder more durable material eg reptile scales

What is the purpose of cysteine in keratin

Creates disulphide bridges. Strong binding units that resist large deformations and return the protein to a functioning shape. Most important in highly flexible systems eg hair

Explain the effect of heat on hair

Heat breaks the H bond altering structure quickly removing heat quickly achieves different structure

Explain how pre stressing prevents cracks

Pre stress avoids low stress strain region of mechanics, so far more force required for strain. Or more materials stress condition so atoms have to be moved initially out of stress state

Why does defocussing of crack tip reduce localised strain energy

Material has preferred interfaces, particular strain directions (ie how atoms will distort) which means crack tip is defocussed or broadened, Thus strain energy reduced due to smaller atom displacements

What is the effect of convolution of material on cracks

Surface generated larger increasing surface energy and inhibiting crack growth

Explain the effect of convolution of material on cracks

Imbalance of bonds eg molecular units different h bonds combinations etc. So variation of energy required to break bonds for crack to propagate. It is forced to displace in direction to weaker bonds creating a wavy surface which has a larger surface area thus higher energy penalty

Explain how fibres in material reorientate around crack tip

Fibres realign in presence of strain to sit perp across crack front. This inhibits crack growth as it must move around fibre or induce large configurational change in fibre

What are 3 layers of skin

Epidermis, dermis, hypodermis

Explain the epidermis

Tough outer coating hard to penetrate. Large quantity of keratinocytes - large quantities of alpha keratin

Explain the dermis

Main functional region with connective tissue. Lots of collagen which holds layers and content together due to flexibility of toe region

Explain the hypodermis

Loose connective tissue with lots of fat content. Highly elastic component that will deform under stress.

What are Langer's Lines

Anatomical lines that indicate the natural orientation of collagen fibres in the skin. Skin is anisotropic. When it is punctured, the holes are elongated because skin is much stiffer along the lines than across them.

Why are Langer's Lines useful

Deciding how to make an incision, cutting along the line heals better and shows reduced scarring

What are burns?

Heat damage to biological material. Will induce denaturation at low levels and then bond breakage with further heat.

What happens in a first degree burn?

Destroyed epidermis

What happens in a second degree burn?

Destroyed epidermis and some dermis, tissue remains around hair follicles for regeneration with scarring

What happens in a third degree burn?

Skin fully destroyed leaving only fat and muscle

What is a graft?

Take healthy skin that contain all the epidermis and part of the dermis and place on to damaged area. Only a small amount of skin can be moved. Process can lead to infection, bleeding and nerve damage.

What's the reaction of organism to a biotoxic material

Atrophy, pathological change or rejection of living tissue

What's the reaction of organism to a bioinert material

Coexistence of material without noticeable change. Separation by a layer of fibrous tissue

What's the reaction of organism to a bioactive material

Formation of direct bonds with material and free growth

What's the reaction of organism to a bioresorbable material

Gradual dissolution of the material by the biosystem, replacement without toxicity or rejection

What is tissue engineering

Repair, regeneration or replacement of damaged or diseased tissues to their original state and function.

For tissue engineering why do we want materials that are porous/low density

To allow egress (going in/out) and dissolution attack by body

Why are Polyglycolic/polylactic acids good biomaterials

Degrade to glycolic and lactic acid. Natural molecules found in the body.

Explain the structure of integra (burn healing)

Bilayer structure: Top layer silicone sheet – provides protection to wound during healing. Bottom layer collagen sponge – support layer for growth of new dermis. Top layer of sheet removed and epithelial cells applied to wound area for intergrowth.

How do sea cucumbers increase stiffness as a defence mechanism

Ion charge density shifts towards stiff response. E.g. Ca, Mg present for stiff response. Few ions present for soft response. Ions can act as bridges between polymers chains creating cross-links. Polymer system becomes much stiff with additional bonding.

What are biominerals?

Mineral structures made by organisms, composites

What two systems are biominerals composites of

Ionic solids (matrix) and biological polymers (fibres)

Why do most biominerals not follow Voigt and Reuss limit closely

Due to multi orientation of fibres, also hierarchical structure ie not simply two component mix but mix at multiple length scales

When is Voigt Limit used

Materials is stretched axially. Both components must strain equally if integrity is to be maintained.

When is Reuss Limit used

Materials is stretched transverse. Now both components are subjected to the same stress.

What factors control the constructure of mineral phases

Natural abundance, availability of elements, thermal stability of minerals so can form at room temp

What is Enamel made from

95% hydroxyapatite mineral, 4% water, 1% biological molecules

What is Dentine made from

50% hydroxyapatite mineral, 20% water, 30% biological molecules

What's the Mohr hardness of enamel and dentine

Enamel: 5, Dentine: 3

What are tubules

Cellular structures but not live cells

NEED QUESTION

Tubules (cellular structures but not live cells) surrounded with

collagen fibrils that are coated with hydroxyapatite tablets

NEED QUESTION

Micro regions to hinder crack propagation. Anistropic structure hinder passage of crack. Mineral tablets compressed in c-axis via association with collagen. Hinders crack growth within mineral

What polymer is used for dental implants

Polymethylmethacrylate (plexiglass/perspex).

Explain PMMA as a dental implant

Tough and shatter resistant material. Chemically highly resistant. Whole system can be constructed from polymer avoiding adhesion issues

What are fillings used for?

Used to prevent further bacterial/chemical attack to tooth. Essentially a protective coating

Explain amalgams fillings

Alloy mix of tin, silver and mercury formed via eutectic type process. Working from liquid and powder makes filling gap relatively straightforward and quick

Disadvantages of amalgams

Binding between amalgam and tooth weak so potential mechanical issues. Health scares around Hg use. General appearance and discolouration with corrosion an issue

Explain composite cements for modern fillings

Matrix – polyacrylate. Filler – glass ionomer cement – aluminosilicate glass. Acid groups of polymer will attack glass and leach out ions – create bridging effect between matrix and filler to strengthen bond.

Explain composite resins for modern fillings

Matrix – photocurable polymer. Filler – reinforcing particles such as silica and TiO2. Coupling agent 0 promotes adhesion between filler and matrix. UV source used to polymerise resin and set whole material

State the corrosion equations for iron

Fe + 2H+ = Fe2+ + H2

2Fe + 4H+ + O2 = 2Fe2+ + 2H2O

2Fe + 2H2O + O2 = 2Fe2+ + 4OH-

Why are biological environments highly corrosive

Water based with lots of acids present

State the different functions of bone

Protection, sound transmission, blood production, mineral store, motion and support

Where is bone used for protection

Skull, rib cage

Where is bone used for sound transmission

Auditory ossicles

Explain the use of bone for blood production

Marrow produces blood cells

State what minerals are stored in bone

Calcium and phosphorus (the bone also controls phosphate metabolism), heavy metals (detoxification) and other metabolic functions.

How are bones used for motion and support

Bones are lever arms pivoting around the joints that act as a fulcrum. Bones are attached to each other by fibrous, cartilaginous and synovial joints. Only the third permits significant motion